Previous studies have led to a picture wherein the replication of DNA progresses at variable rates over different parts of the budding yeast genome. These prior experiments, focused on production of nascent DNA, have been interpreted to imply that the dynamics of replication fork progression are strongly affected by local chromatin structure/architecture, and by interaction with machineries con...

Inactivated replication forks may be reversed by the annealing of leading- and lagging-strand ends, resulting in the formation of a Holliday junction (HJ) adjacent to a DNA double-strand end. In Escherichia coli mutants deficient for double-strand end processing, resolution of the HJ by RuvABC leads to fork breakage, a reaction that we can directly quantify. Here we used the HJ-specific resolva...

In this paper we show that the class of fork squares has a complete orthodox axiomatization in fork arrow logic (FAL). This result may be seen as an orthodox counterpart of Venema’s non-orthodox axiomatization for the class of squares in arrow logic. FAL is the modal logic of fork algebras (FAs) just as arrow logic is the modal logic of relation algebras (RAs). FAs extend RAs by a binary fork o...

Fewer forks make faster progress J ust as a large number of forks can inhibit someone unaccustomed to formal dining, an excess of replication forks can slow the rate of DNA synthesis, Zhong et al. reveal. Cdc7 is the catalytic subunit of the Dbf4-dependent kinase, which initiates DNA replication by activating the DNA helicase complex MCM at replication origins. In response to DNA damage, the ch...

Replication fork protection complex Swi1-Swi3 and replication checkpoint mediator Mrc1 are required for maintenance of replication fork integrity during the course of DNA replication in the fission yeast Schizosaccharomyces pombe. These proteins play crucial roles in stabilizing stalled forks and activating replication checkpoint signaling pathways. Although they are conserved replication fork ...

State-space search with explicit abstraction heuristics is at the state of the art of costoptimal planning. These heuristics are inherently limited, nonetheless, because the size of the abstract space must be bounded by some, even if a very large, constant. Targeting this shortcoming, we introduce the notion of (additive) implicit abstractions , in which the planning task is abstracted by insta...

a preformed replication fork. The preformed replication fork consisted of a nicked, double-stranded, circular DNA molecule with a 5' single-strand tail that was noncomplementary to the template. The products of DNA synthesis on this substrate were rolling-circle molecules, as demonstrated by electron microscopy and alkaline agarose gel electrophoresis. The tails contained double-stranded region...

One of the central problems in matroid theory is Rota's conjecture that, for all prime powers q, the class of GF(q)-representable matroids has a finite set of excluded minors. This conjecture has been settled for q s; 4 but remains open otherwise. Further progress towards this conjecture has been hindered by the fact that, for all q > 5, there are 3-connected GF(q)-representable matroids having...

Manual garden tools help a lot with different types of work soil: digging, removing roots and weeds, harvesting root crops bulbs, much more would be difficult if it were not for the forks. This tool has wide range features. There are many varieties this differing in shapes sizes: manure, harvesting, hay, flower, pointed, fork-shovel, telescopic, ball-pointed. A common problem all manual forks i...

Mammalian RAD51 paralogs are implicated in the repair of collapsed replication forks by homologous recombination. However, their physiological roles in replication fork maintenance prior to fork collapse remain obscure. Here, we report on the role of RAD51 paralogs in short-term replicative stress devoid of DSBs. We show that RAD51 paralogs localize to nascent DNA and common fragile sites upon ...